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- PDB-2mb3: Solution structure of an intramolecular (3+1) human telomeric G-q... -

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Basic information

Entry
Database: PDB / ID: 2mb3
TitleSolution structure of an intramolecular (3+1) human telomeric G-quadruplex bound to a telomestatin derivative
ComponentsDNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')
KeywordsDNA/DNA INHIBITOR / intramolecular G-quadruplex / human telomere / anticancer targets / macrocyclic hexaoxazole / telomestatin derivative / DNA-DNA INHIBITOR complex
Function / homologyChem-L2H / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsChung, W.J. / Heddi, B. / Tera, M. / Iida, K. / Nagasawa, K. / Phan, A.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Solution structure of an intramolecular (3 + 1) human telomeric g-quadruplex bound to a telomestatin derivative.
Authors: Chung, W.J. / Heddi, B. / Tera, M. / Iida, K. / Nagasawa, K. / Phan, A.T.
History
DepositionJul 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nmr_software / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_nmr_data / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2792
Polymers7,5921
Non-polymers6871
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')


Mass: 7591.883 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-L2H / (12S,27S)-12,27-bis(4-aminobutyl)-4,30-dimethyl-3,7,14,18,22,29-hexaoxa-11,26,31,32,33,34,35,36-octaazaheptacyclo[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]hexatriaconta-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-dode caene-10,25-dione / Telomestatin derivative


Mass: 686.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H34N10O8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3122D 1H-1H TOCSY
3212D 1H-1H TOCSY
3312D 1H-1H NOESY
3422D 1H-1H NOESY
1522D 1H-1H NOESY
2622D 1H-1H NOESY
3722D 1H-13C HSQC aromatic
2852D 1H-13C HSQC aromatic
3922D 1H-13C HSQC aliphatic
21052D 1H-13C HSQC aliphatic
21142D 1H-13C HSQC aliphatic
21242D 1H-13C HSQC aromatic
21331D JRHMBC
31422D 1H-31P HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 90% H2O/10% D2O90% H2O/10% D2O
20.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 100% D2O100% D2O
30.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 90% H2O/10% D2O90% H2O/10% D2O
40.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 100% D2O100% D2O
50.2-1 mM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 mM L2H, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')-10.2-21
mML2H-20.2-21
mMDNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')-30.2-22
mML2H-40.2-22
0.2 mMDNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')-5[U-99% 13C; U-99% 15N]3
0.2 mML2H-63
0.2 mMDNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')-7[U-99% 13C; U-99% 15N]4
0.2 mML2H-84
mMDNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')-9[U-4% 13C]0.2-15
mML2H-100.2-15
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1907ambient atm310 K
2907298 K
3407298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX7002
Bruker AMXBrukerAMX4003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollmanrefinement
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TopSpinBruker Biospincollection
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 579 / NOE intraresidue total count: 279
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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